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- PDB-8zwd: Crystal structure of methanol dehydrogenase1 from Bacillus methan... -

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Basic information

Entry
Database: PDB / ID: 8zwd
TitleCrystal structure of methanol dehydrogenase1 from Bacillus methanolicus
ComponentsNAD(P)-dependent methanol dehydrogenase
KeywordsOXIDOREDUCTASE / methanol dehydrogenase / TypeIII alcohol dehydrogenase
Function / homology
Function and homology information


methanol dehydrogenase / methanol dehydrogenase (NAD+) activity / metal ion binding
Similarity search - Function
Iron-type alcohol dehydrogenase-like / Iron-containing alcohol dehydrogenases signature 2. / Iron-containing alcohol dehydrogenases signature 1. / Alcohol dehydrogenase, iron-type, conserved site / Alcohol dehydrogenase, iron-type/glycerol dehydrogenase GldA / Iron-containing alcohol dehydrogenase
Similarity search - Domain/homology
: / NAD(P)-dependent methanol dehydrogenase
Similarity search - Component
Biological speciesBacillus methanolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsMa, B.D. / Kong, X.D.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2021YFA0911000 China
CitationJournal: To Be Published
Title: Crystal structure of methanol dehydrogenase1 from Bacillus methanolicus
Authors: Ma, B.D. / Kong, X.D.
History
DepositionJun 12, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 18, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: NAD(P)-dependent methanol dehydrogenase
D: NAD(P)-dependent methanol dehydrogenase
H: NAD(P)-dependent methanol dehydrogenase
J: NAD(P)-dependent methanol dehydrogenase
E: NAD(P)-dependent methanol dehydrogenase
G: NAD(P)-dependent methanol dehydrogenase
F: NAD(P)-dependent methanol dehydrogenase
C: NAD(P)-dependent methanol dehydrogenase
A: NAD(P)-dependent methanol dehydrogenase
I: NAD(P)-dependent methanol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)413,48122
Polymers412,86010
Non-polymers62012
Water28816
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)256.022, 83.578, 220.557
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
NAD(P)-dependent methanol dehydrogenase / NAD-dependent methanol dehydrogenase


Mass: 41286.047 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus methanolicus (bacteria) / Gene: mdh, BMMGA3_17200 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6TV41, methanol dehydrogenase
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.86 Å3/Da / Density % sol: 56.96 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2 M sodium malonate, 0.1 M Bis Tris propane 7.2, 23 % w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979183 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jan 13, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 3→255.07 Å / Num. obs: 94482 / % possible obs: 100 % / Redundancy: 3.8 % / CC1/2: 0.839 / Rmerge(I) obs: 0.207 / Rpim(I) all: 0.124 / Rrim(I) all: 0.242 / Χ2: 1.25 / Net I/σ(I): 6.8 / Num. measured all: 359438
Reflection shellResolution: 3→3.05 Å / % possible obs: 100 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.386 / Num. measured all: 17935 / Num. unique obs: 4649 / CC1/2: 0.795 / Rpim(I) all: 0.229 / Rrim(I) all: 0.449 / Χ2: 0.98 / Net I/σ(I) obs: 3.9

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→29.78 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2603 4516 4.95 %
Rwork0.2133 --
obs0.2156 91256 95.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→29.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27930 0 12 16 27958
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01128358
X-RAY DIFFRACTIONf_angle_d1.30638497
X-RAY DIFFRACTIONf_dihedral_angle_d5.3483950
X-RAY DIFFRACTIONf_chiral_restr0.0714612
X-RAY DIFFRACTIONf_plane_restr0.0235026
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.030.42811390.31142983X-RAY DIFFRACTION100
3.03-3.070.33141420.2933021X-RAY DIFFRACTION100
3.07-3.110.3411530.29223005X-RAY DIFFRACTION100
3.11-3.150.36151750.28142947X-RAY DIFFRACTION100
3.15-3.190.34631680.27123002X-RAY DIFFRACTION100
3.19-3.230.33711520.26712986X-RAY DIFFRACTION100
3.23-3.280.31081590.25742949X-RAY DIFFRACTION100
3.28-3.330.31891790.25453009X-RAY DIFFRACTION100
3.33-3.380.35391790.26612974X-RAY DIFFRACTION100
3.38-3.430.31471600.26072951X-RAY DIFFRACTION100
3.43-3.490.3367690.2981422X-RAY DIFFRACTION47
3.49-3.560.26311640.22792983X-RAY DIFFRACTION100
3.56-3.620.27631340.2183035X-RAY DIFFRACTION100
3.62-3.70.2915890.24121718X-RAY DIFFRACTION58
3.7-3.780.28651490.23253034X-RAY DIFFRACTION100
3.78-3.870.27441560.22883008X-RAY DIFFRACTION100
3.87-3.960.2689970.2241963X-RAY DIFFRACTION65
3.96-4.070.29341520.20582992X-RAY DIFFRACTION100
4.07-4.190.25721490.20363044X-RAY DIFFRACTION100
4.19-4.320.22541750.22955X-RAY DIFFRACTION100
4.32-4.480.24911570.18643023X-RAY DIFFRACTION100
4.48-4.660.20931520.17973031X-RAY DIFFRACTION99
4.66-4.870.20721650.18672988X-RAY DIFFRACTION100
4.87-5.120.24821430.19443077X-RAY DIFFRACTION100
5.12-5.440.26051680.21363016X-RAY DIFFRACTION100
5.44-5.860.27221570.21593060X-RAY DIFFRACTION100
5.86-6.440.25661470.21673105X-RAY DIFFRACTION100
6.44-7.360.25411480.1933085X-RAY DIFFRACTION100
7.36-9.230.18161570.15083139X-RAY DIFFRACTION99
9.23-29.780.18991820.18183235X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -38.0204 Å / Origin y: -57.0597 Å / Origin z: -10.9852 Å
111213212223313233
T0.1804 Å20.0054 Å20.0436 Å2-0.1391 Å20.0168 Å2--0.1749 Å2
L0.1103 °20.0105 °2-0.0498 °2-0.0065 °20.0247 °2--0.1287 °2
S-0.0034 Å °-0.0095 Å °-0.0101 Å °0.0297 Å °-0.0052 Å °0.0084 Å °0.0294 Å °0.0054 Å °0 Å °
Refinement TLS groupSelection details: all

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